Molecular and Population Genetic Analyses of Coat in Nigerian Goats

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Adefenwa, F.A
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This research was aimed at investigating the relationship between coat colour and some body traits in Nigerian goats, identify mutations in some mammalian coat colour genes in goats, determine the relationship between such variations and coat colour differences among Nigerian and some American goat breeds, and validate the association between identified mutations and some body traits in Nigerian goats. Data on body weight and some linear body measurements were collected from West African Dwarf, Red Sokoto and Sahel goats from different states across Nigeria. Multivariate analysis of variance using the General Linear Model (GLM) procedure of SPSS (2010) was carried out for body weight and all the linear body measurements. Coat colour was found to significantly (P<0.05) affect body weight, body length and heart girth. Three single nucleotide polymorphisms (SNPs), two missense mutations; p.E55K and p.N56K; and one silent mutation, g.221T>C, were identified, upon amplification and sequencing, within a 684 bp fragment spanning part of the coding region of the MC1R gene in Nigerian goats. Both missense mutations were present only in the WAD goat. Among American goats, five single nucleotide polymorphisms (SNPs), four missense mutations; p.S52R, p.E55K, p.K226E and p.R229P; and one silent mutation, g.221C>T, were identified within the same 684 bp region. The missense mutations p.S52R and p.E55K were found to be specific to the Alpine breed while p.K226E and p.R229P were found only in the Spanish breed. The missense mutation p.E55K was identified in both xvii populations and was found to be specific to the WAD goat (mostly black) and the Alpine breed (black and white). A 352 bp fragment spanning part of exon 2 and the whole intron 2 of the ASIP gene was amplified and sequenced in Nigerian and American goats. Nine mutations; three intronic, one silent and five missense (p.S19R, p.N35K, p.L36V, p.M42L and p.L45W) mutations were identified in Nigerian goats. About 89% of the animals were found to carry the wild type allele. In the American goats, two intronic mutations, g.293G>A and g.327C>A, were identified. The results from the studies on MC1R and ASIP genes seem to support the hypothesis of epistatic interaction between MC1R and ASIP, i.e., the possibility to express the ASIP alleles can be obtained only when at least a copy of a putative wild type allele at the MC1R locus is present. The white phenotype in the Saanen and Sahel goats maybe due to the presence of the Awt allele at the ASIP locus as described in other goat breeds with white coat colour. The g.293G>A and g.327C>A mutations found in the American breeds seem to be specific to the Alpine breed. These mutations might therefore contribute to the black colour observed in this breed. No significant differences were found to exist between Nigerian breeds for the g.469C>G mutation at the MLPH locus. Lack of association between genotypes at the MC1R locus and morphological traits was also observed in this study According to the results obtained from these studies, mutations at the MC1R and ASIP loci may determine eumelanic and phaeomelanic phenotypes. They are, however, probably not the only factors. Other genes might be involved in determining red coat colour especially. xviii 1.0 Introduction and Background of Study Livestock are found everywhere in poor communities across the developing world. An estimated two-thirds of households in rural communities keep some type of livestock (Randolph et al., 2007). Similar information for poor urban households is scarce, but according to Randolph et al. (2007), a recent survey in two cities in Nigeria found that more than one-half of all urban households were keeping livestock; the highest rates were found in the most densely populated, lower-income areas. Small ruminants, goats and sheep, when compared to other livestock species, are extremely important within most farming systems (Djajanegara et al., 1996). Small ruminants are relatively easy to own by resource poor farmers especially women because of their small size and early maturity that makes them suitable for meeting subsistence needs for meat and milk. Raising small ruminants is regarded as relatively easy with minimal inputs and low maintenance costs coupled with their ability to maximise available feed resources. In most cases it is basically a secondary activity that employs low levels of family resources (Nwafor, 2004). Particular advantages of small ruminants over large ruminants include higher production efficiency, easier marketability and lower risks (Soedjana et al., 1988), broader adaptability to different environments, and smaller absolute feed requirements per animal (Peters, 1988). Small ruminants contribute immensely to the general economy of nations. Raising of small ruminants is an important economic activity from which food (meat, milk) and non-food commodities (manure, hides and skin, wool, etc) and cash income are derived. 1 Goats are renowned for their hardiness and prolificacy. Sheep are grazers and amenable to herding. On the other hand, goats are browsers and have the ability to thrive even when feed resources, except bushes and shrubs, appear to be non-existent (Devandra, 1989). Goats have higher survival rates under drought conditions. They can still provide a reasonable amount of production with every four days watering routine (Mengistu, 2007). There is an apparent consumers‟ preference for goat meat and mutton over available substitutes in most parts of West Africa. This preference is mainly associated to the taste of the meat, the dietary variety, as well as consumers‟ cultural and religious considerations (Sumberg and Cassaday, 1985). There is a growing increase in human population and if the production of livestock continues at its present rate, the increase in livestock production will ultimately lag behind the ever-growing human population. The Food and Agriculture Organization (FAO) in 1990 estimated that animal production should be increased by 4% annually to meet the demand of the human population. The major factors that affect the productivity of goats, and small ruminants in general, in Sub-Saharan Africa are feed supply, genotype, animal management, policy and institutional constraints (Ibrahim, 1998; Peacock and Sherman, 2008). The major feed resource which is natural pasture shows remarkable seasonality in yield and quality and lacks the major nutrients that support animal growth particularly during the dry season (Ibrahim, 1998; Peacock and Sherman, 2008). There is a high demand for goat meat globally and with such a high demand, research should be tailored towards providing adequate information on suitable genotypes, improved management practices and other relevant packages (Ibrahim, 1998; Peacock and Sherman, 2008). 2 Goats (Capra hircus) are found across all agro-ecological environments and in nearly all livestock production systems. They are suitable for very extensive to highly mechanized production systems. They are the most adaptable and geographically widespread livestock species, ranging from the mountains of Siberia to the deserts and tropics of Africa (Luikart et al., 2001). The origin of the domestic goat remains controversial but archaeological evidence suggests that they were probably first domesticated about 10,000 years ago in the Fertile Crescent region of the Near East (Luikart et al., 2001). As a result of both natural selection and selective breeding, certain characteristics in certain populations of goats have been reinforced, giving rise to different goat types and breeds. The wild ancestors of the present day goat and many other mammalian livestock were of varying colours. However, uniform colour has been established with very intense selective breeding to make coat colour a major breed characteristic. As a result of artificial selection, some coat colours have reached higher frequencies in certain breeds of mammals than others (Norris and Whan, 2009). Pigmentation of the skin and hair serves a number of valuable functions. Foremost is the photoprotection of underlying tissues from ultraviolet (UV) radiation (Costin and Hearing, 2007; Deng et al., 2009). Recent studies have also shown that melanin not only functions as a sunscreen to absorb UV light and prevent DNA damage, but that its other properties, e.g. as an antioxidant and a radical scavenger, also play important roles in protecting cells from such damage (Costin and Hearing, 2007; Deng et al., 2009). Coat colour in mammals has been associated with productivity and environmental adaptation (King et al., 1988; Becerril et al., 1993; Acharya et al., 1995; Singh et al., 1997). For example, the light coloured hair coat and darkly pigmented skin found in some cattle in tropical places have helped in the adaptability of these animals to high levels of solar radiation encountered in tropical climates (Acharya et al., 1995). Also, the percentage of white colour on Holstein cows has been reported to have a beneficial impact on milk yield and reproductive traits in regions of high solar radiation due to decreased absorption of incident solar radiation resulting in reduced heat stress (Becerril et al., 1993). Singh et al. (1997) reported that the dark coat colour in Indian desert goats serves as an adaptation mechanism to economize feed energy during cool periods. Other performance traits like weight and various other body measurements, such as body length; shoulder width; head width; etc, have been shown to have a relationship with coat colour (Odubote, 1994; Ebozoje and Ikeobi, 1998; Ozoje and Mgbere, 2002). Coat colour has also served as an important form of camouflage and an integral part of social communication and recognition in many mammalian species (Norris and Whan, 2009). Biochemical and molecular studies of coat colour started a decade ago with much of it in mice because of its use as an animal model (Barsh et al., 2000; Mohanty et al., 2008). Relatively little research have, however, been carried out on other mammals such as cattle, pig, horse and goat. From previous studies, over 120 genes have been identified to be responsible for coat colour in mice (Gutiérrez-Gil et al., 2007).
A Thesis Submitted to the School of Postgraduate Studies, University of Lagos
Biochemical and molecular studies , Goats , Mutations , Multivariate analysis of variance , General Linear Model , Research Subject Categories::FORESTRY, AGRICULTURAL SCIENCES and LANDSCAPE PLANNING::Animal production::Animal breeding
Adefenwa, F.A (2011). Molecular and Population Genetic Analyses of Coat in Nigerian Goats. A Thesis Submitted to University of Lagos School of Postgraduate Studies Phd Thesis and Dissertation, 221pp.